--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peptideGenomicCoodinate.py	Fri Apr 06 18:27:47 2018 -0400
@@ -0,0 +1,150 @@
+
+# 
+# Author: Praveen Kumar
+# University of Minnesota
+#
+# Get peptide's genomic coordinate from the protein's genomic mapping sqlite file (which is derived from the https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec)
+# 
+# python peptideGenomicCoordinate.py <peptide_list> <mz_to_sqlite DB> <genomic mapping file DB> <output.bed>
+# 
+#
+
+def main():
+    import sys
+    import sqlite3
+    conn = sqlite3.connect(sys.argv[2])
+    c = conn.cursor()
+    c.execute("DROP table if exists novel")
+    conn.commit()
+    c.execute("CREATE TABLE novel(peptide text)")
+    pepfile = open(sys.argv[1],"r")
+
+    for seq in pepfile.readlines():
+        seq = seq.strip()
+        c.execute('INSERT INTO novel VALUES ("'+seq+'")')
+        conn.commit()
+
+    c.execute("SELECT distinct psm.sequence, ps.id, ps.sequence from db_sequence ps, psm_entries psm, novel n, proteins_by_peptide pbp where psm.sequence = n.peptide and pbp.peptide_ref = psm.id and pbp.id = ps.id")
+    rows = c.fetchall()
+
+    conn1 = sqlite3.connect(sys.argv[3])
+    c1 = conn1.cursor()
+
+    outfh = open(sys.argv[4], "w")
+
+    master_dict = {}
+    for each in rows:
+        peptide = each[0]
+        acc = each[1]
+        acc_seq = each[2]
+    
+        c1.execute("SELECT chrom,start,end,name,strand,cds_start,cds_end FROM feature_cds_map map WHERE map.name = '"+acc+"'")
+        coordinates = c1.fetchall()
+    
+        if len(coordinates) != 0:
+            pep_start = 0
+            pep_end = 0
+            flag = 0
+            splice_flag = 0
+            spliced_peptide = []
+            for each_entry in coordinates:
+                chromosome = each_entry[0]
+                start = int(each_entry[1])
+                end = int(each_entry[2])
+                strand = each_entry[4]
+                cds_start = int(each_entry[5])
+                cds_end = int(each_entry[6])
+                pep_pos_start = (acc_seq.find(peptide)*3)
+                pep_pos_end = pep_pos_start + (len(peptide)*3)
+                if (pep_pos_start >= cds_start) and (pep_pos_end <= cds_end):
+                    if strand == "+":
+                        pep_start = start + pep_pos_start - cds_start
+                        pep_end = start + pep_pos_end - cds_start
+                        pep_thick_start = 0
+                        pep_thick_end = len(peptide)
+                        flag == 1
+                    else:
+                        pep_end = end - pep_pos_start + cds_start
+                        pep_start = end - pep_pos_end + cds_start
+                        pep_thick_start = 0
+                        pep_thick_end = len(peptide)
+                        flag == 1
+                    spliced_peptide = []
+                    splice_flag = 0
+                else:
+                    if flag == 0:
+                        if strand == "+":
+                            if (pep_pos_start >= cds_start) and (pep_pos_start <= cds_end) and (pep_pos_end > cds_end):
+                                pep_start = start + pep_pos_start - cds_start
+                                pep_end = end
+                                pep_thick_start = 0
+                                pep_thick_end = (pep_end-pep_start)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            elif (pep_pos_end >= cds_start) and (pep_pos_end <= cds_end) and (pep_pos_start < cds_start):
+                                pep_start = start
+                                pep_end = start + pep_pos_end - cds_start
+                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
+                                pep_thick_end = (len(peptide)*3)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            else:
+                                pass
+                        else:
+                            if (pep_pos_start >= cds_start) and (pep_pos_start <= cds_end) and (pep_pos_end >= cds_end):
+                                pep_start = start
+                                pep_end = end - pep_pos_start - cds_start
+                                pep_thick_start = 0
+                                pep_thick_end = (pep_end-pep_start)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            elif (pep_pos_end >= cds_start) and (pep_pos_end <= cds_end) and (pep_pos_start <= cds_start):
+                                pep_start = end - pep_pos_end + cds_start
+                                pep_end = end
+                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
+                                pep_thick_end = (len(peptide)*3)
+                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
+                                splice_flag = splice_flag + 1
+                                if splice_flag == 2:
+                                    flag = 1
+                            else:
+                                pass
+            if len(spliced_peptide) == 0:
+                if strand == "+":
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
+                else:
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
+                outfh.write("\t".join(bed_line)+"\n")
+            else:
+                if strand == "+":
+                    pep_entry = spliced_peptide
+                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
+                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
+                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
+                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
+                    outfh.write("\t".join(bed_line)+"\n")
+                else:
+                    pep_entry = spliced_peptide
+                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
+                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
+                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
+                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
+                    bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
+                    outfh.write("\t".join(bed_line)+"\n")
+    c.execute("DROP table novel")
+    conn.commit()
+    conn.close()
+    conn1.close()
+    outfh.close()
+    pepfile.close()
+    
+    return None
+if __name__ == "__main__":
+    main()